High‐molecular‐weight DNA extraction for long‐read sequencing of plant genomes: An optimization of standard methods

Abstract

Abstract Premise Developing an effective and easy‐to‐use high‐molecular‐weight (HMW) DNA extraction method is essential for genomic research, especially in the era of third‐generation sequencing. To efficiently use technologies capable of generating long‐read sequences, it is important to maximize both the length and purity of the extracted DNA; however, this is frequently difficult to achieve with plant samples. Methods and Results We present a HMW DNA extraction method that combines (1) a nuclei extraction method followed by (2) a traditional cetyltrimethylammonium bromide (CTAB) DNA extraction method for plants with optimized extraction conditions that influence HMW DNA recovery. Our protocol produced DNA fragments (percentage of fragments >20 kbp) that were, on average, ca. five times longer than those obtained using a commercial kit, and contaminants were removed more effectively. Conclusions This effective HMW DNA extraction protocol can be used as a standard protocol for a diverse array of taxa, which will enhance plant genomic research.

Keywords

• CTAB
• DNA extraction
• Femto Pulse system
• high‐molecular‐weight DNA
• nuclei extraction